Linking Nitrogen Load to the Structure and Function of Wetland Soil and Rhizosphere Microbial Communities

Biogeography and impact of nitrous oxide reducers in rivers across a broad environmental gradient on emission rates

Microbial communities that reduce nitrous oxide (N2O) are divided into two clades, nosZI and nosZII. These clades significantly differ in their ecological niches and their implications for N2O emissions in terrestrial environments. However, our understanding of N2O reducers in aquatic systems is currently limited. This study investigated the relative abundance and diversity of nosZI- and nosZII-type N2O reducers in rivers and their impact on N2O emissions. Our findings revealed that stream sediments possess a high capacity for N2O reduction, surpassing N2O production under high N2O/NO3- ratio conditions. This study, along with others in freshwater systems, demonstrated that nosZI marginally dominates more often in rivers. While microbes containing either nosZI and nosZII were crucial in reducing N2O emissions, the net contribution of nosZII-containing microbes was more significant. This can be attributed to the nir gene co-occurring more frequently with the nosZI gene than with the nosZII gene. The diversity within each clade also played a role, with nosZII species being more likely to function as N2O sinks in streams with higher N2O concentrations. Overall, our findings provide a foundation for a better understanding of the biogeography of stream N2O reducers and their effects on N2O emissions.

The effect of anaerobic digestate as an organic soil fertilizer on the diversity and structure of the indigenous soil microbial and nematode communities

Anaerobic digestate is a popular soil additive which can promote sustainability and transition toward a circular economy. This study addresses how anaerobic digestate modifies soil health when combined with a common chemical fertilizer. Attention was given to soil microbes and, a neglected but of paramount importance soil taxonomic group, soil nematodes. A mesocosm experiment was set up in order to assess the soil's microbial and nematode community. The results demonstrated that the microbial diversity was not affected by the different fertilization regimes, although species richness increased after digestate and mixed fertilization. The composition and abundance of nematode community did not respond to any treatment. Mixed fertilization notably increased potassium (K) and boron (B) levels, while nitrate (NO3-) levels were uniformly elevated across fertilized soils, despite variations in nitrogen input. Network analysis revealed that chemical fertilization led to a densely interconnected network with mainly mutualistic relationships which could cause ecosystem disruption, while digestate application formed a more complex community based on bacterial interactions. However, the combination of both orchestrated a more balanced and less complex community structure, which is more resilient to random disturbances, but on the downside, it is more likely to collapse under targeted perturbations.

Potential synergy of microplastics and nitrogen enrichment on plant holobionts in wetland ecosystems

Wetland ecosystems are global hotspots for environmental contaminants, including microplastics (MPs) and nutrients such as nitrogen (N) and phosphorus (P). While MP and nutrient effects on host plants and their associated microbial communities at the individual level have been studied, their synergistic effects on a plant holobiont (i.e., a plant host plus its microbiota, such as bacteria and fungi) in wetland ecosystems are nearly unknown. As an ecological entity, plant holobionts play pivotal roles in biological nitrogen fixation, promote plant resilience and defense chemistry against pathogens, and enhance biogeochemical processes. We summarize evidence based on recent literature to elaborate on the potential synergy of MPs and nutrient enrichment on plant holobionts in wetland ecosystems. We provide a conceptual framework to explain the interplay of MPs, nutrients, and plant holobionts and discuss major pathways of MPs and nutrients into the wetland milieu. Moreover, we highlight the ecological consequences of loss of plant holobionts in wetland ecosystems and conclude with recommendations for pending questions that warrant urgent research. We found that nutrient enrichment promotes the recruitment of MPs-degraded microorganisms and accelerates microbially mediated degradation of MPs, modifying their distribution and toxicity impacts on plant holobionts in wetland ecosystems. Moreover, a loss of wetland plant holobionts via long-term MP-nutrient interactions may likely exacerbate the disruption of wetland ecosystems' capacity to offer nature-based solutions for climate change mitigation through soil organic C sequestration. In conclusion, MP and nutrient enrichment interactions represent a severe ecological risk that can disorganize plant holobionts and their taxonomic roles, leading to dysbiosis (i.e., the disintegration of a stable plant microbiome) and diminishing wetland ecosystems' integrity and multifunctionality.

Effects of polyethylene microplastics and heavy metals on soil-plant microbial dynamics

Polyethylene (PE) microplastics are emerging pollutants that pose a significant threat to the environment and human health. However, little is known about the effects of PEs on soil‒plant interactions, especially in heavy metal (HM)-contaminated soil. In this study, the effects of PE on rhizosphere soil enzyme activities, microbial interactions and nutrient cycling processes were analyzed from ecological network and functional gene perspectives for the first time. The results indicated that PE-MP addition significantly reduced the biomass of Bidens pilosa L. In addition, the partial increase in carbon, nitrogen, and phosphorus enzyme activities suggested that the effects of PE as a carbon source on microbial functions in HM-contaminated soil should not be ignored. The average path length of bacterial network nodes was found to be higher than that of fungal network nodes, demonstrating that the bacterial ecological network in PE-MP and HM cocontaminated environments has good buffering capacity against changes in external environmental conditions. Furthermore, structural equation modeling demonstrated that particle size and dosage affect soil nutrient cycling processes and that cycling processes are acutely aware of changes in any factor, such as soil moisture, soil pH and soil nitrogen nutrients. Hence, PE-MP addition in HM-contaminated soil has the potential to alter soil ecological functions and nutrient cycles.

Inducing root redundant development to release oxygen: An efficient natural oxygenation approach for subsurface flow constructed wetland

Dissolved oxygen (DO) is a limiting factor affecting the purification efficiency of subsurface flow (SSF) constructed wetlands (CWs). To clarify the causes of oxygen environments and the response characteristics of plant oxygen release (POR) in SSF CWs, this study set three oxygen source treatments by limiting atmospheric reaeration (AR) and influent oxygen (IO) and compared the differences in plant physiological metabolism, DO distribution characteristics, and the purification effect of the SSF CWs at different depths. The results showed that limiting exogenous oxygen stimulated root redundancy of the wetland plants. The root volume and proportion of fibrous roots of the wetland plants increased significantly (p < 0.05). When only the POR existed, the root zone DO increased significantly to 2.05-4.37 mg/L (p < 0.05), and was positively correlated with the TN and TP removal rates (p < 0.05). Additionally, in the presence of POR only, the average removal rates of TN and TP in the top layer were 86.5% and 76.9%, respectively. The proportion of fibrous roots, root zone DO, and root-shoot ratio were key factors promoting the purification effect of the SSF CWs under limited exogenous oxygen sources. Enhancing POR by inducing root redundancy enhanced nitrification (hao, pmoABC-amoABC), plant absorption, and assimilation-related functional genes (nrtABC, nifKDH), and enriched nitrogen and phosphorus removal bacteria, such as Flavobacterium and Zoogloea. This consequently improved pollutant removal efficiency. Inducing root redundancy to strengthen POR produced an aerobic environment in the SSF CWs. This ensures the efficient and stable operation of the SSF CW and is an effective approach for natural oxygenation.

Nitrate determines the bacterial habitat specialization and impacts microbial functions in a subsurface karst cave

Karst caves are usually considered as natural laboratories to study pristine microbiomes in subsurface biosphere. However, effects of the increasingly detected nitrate in underground karst ecosystem due to the acid rain impact on microbiota and their functions in subsurface karst caves have remained largely unknown. In this study, samples of weathered rocks and sediments were collected from the Chang Cave, Hubei province and subjected to high-throughput sequencing of 16S rRNA genes. The results showed that nitrate significantly impacted bacterial compositions, interactions, and functions in different habitats. Bacterial communities clustered according to their habitats with distinguished indicator groups identified for each individual habitat. Nitrate shaped the overall bacterial communities across two habitats with a contribution of 27.2%, whereas the pH and TOC, respectively, structured bacterial communities in weathered rocks and sediments. Alpha and beta diversities of bacterial communities increased with nitrate concentration in both habitats, with nitrate directly affecting alpha diversity in sediments, but indirectly on weathered rocks by lowering pH. Nitrate impacted more on bacterial communities in weathered rocks at the genus level than in sediments because more genera significantly correlated with nitrate concentration in weathered rocks. Diverse keystone taxa involved in nitrogen cycling were identified in the co-occurrence networks such as nitrate reducers, ammonium-oxidizers, and N₂-fixers. Tax4Fun2 analysis further confirmed the dominance of genes involved in nitrogen cycling. Genes of methane metabolism and carbon fixation were also dominant. The dominance of dissimilatory and assimilatory nitrate reduction in nitrogen cycling substantiated nitrate impact on bacterial functions. Our results for the first time revealed the impact of nitrate on subsurface karst ecosystem in terms of bacterial compositions, interactions, and functions, providing an important reference for further deciphering the disturbance of human activities on the subsurface biosphere.

Archaea and their interactions with bacteria in a karst ecosystem

Karst ecosystems are widely distributed around the world, accounting for 15-20% of the global land area. However, knowledge on microbial ecology of these systems does not match with their global importance. To close this knowledge gap, we sampled three niches including weathered rock, sediment, and drip water inside the Heshang Cave and three types of soils overlying the cave (forest soil, farmland soil, and pristine karst soil). All these samples were subjected to high-throughput sequencing of V4-V5 region of 16S rRNA gene and analyzed with multivariate statistical analysis. Overall, archaeal communities were dominated by Thaumarchaeota, whereas Actinobacteria dominated bacterial communities. Thermoplasmata, Nitrosopumilaceae, Aenigmarchaeales, Crossiella, Acidothermus, and Solirubrobacter were the important predictor groups inside the Heshang Cave, which were correlated to NH₄ ⁺ availability. In contrast, Candidatus Nitrososphaera, Candidatus Nitrocosmicus, Thaumarchaeota Group 1.1c, and Pseudonocardiaceae were the predictors outside the cave, whose distribution was correlated with pH, Ca²⁺, and NO₂ ^-. Tighter network structures were found in archaeal communities than those of bacteria, whereas the topological properties of bacterial networks were more similar to those of total prokaryotic networks. Both chemolithoautotrophic archaea (Candidatus Methanoperedens and Nitrosopumilaceae) and bacteria (subgroup 7 of Acidobacteria and Rokubacteriales) were the dominant keystone taxa within the co-occurrence networks, potentially playing fundamental roles in obtaining energy under oligotrophic conditions and thus maintaining the stability of the cave ecosystem. To be noted, all the keystone taxa of karst ecosystems were related to nitrogen cycling, which needs further investigation, particularly the role of archaea. The predicted ecological functions in karst soils mainly related to carbohydrate metabolism, biotin metabolism, and synthesis of fatty acid. Our results offer new insights into archaeal ecology, their potential functions, and archaeal interactions with bacteria, which enhance our understanding about the microbial dark matter in the subsurface karst ecosystems.

Fecal microbiota transplants modulate the gut microbiome of a two-toed sloth (Choloepus didactylus)

The microbes inhabiting an animal's gastrointestinal tracts, collectively known as the gut microbiome, are vital to animal health and wellbeing. For animals experiencing gut distress or infection, modulation of the gut microbiome, for example, via fecal microbiota transplant (FMT), provides a possible disease prevention and treatment method. The beneficial microbes present in the donor's transplanted feces can help combat pathogens, assist in digestion, and rebalance the recipient's microbiota. Investigating the efficacy of FMTs in animal health is a crucial step toward improving management strategies for species under human care. We present a case study of the use of FMTs in a two-toed sloth experiencing abnormally large, clumped, and frequent stools. We used 16 S rRNA amplicon sequencing of fecal samples to (a) compare the microbiomes of the FMT donor, a healthy, cohoused conspecific, and the FMT recipient and (b) assess the influence of multiple rounds of FMTs on the recipient's microbiome and stool consistency and frequency over time. In response to the FMTs, we found that the recipient's microbiome showed trends toward increased diversity, shifted community composition, and altered membership that more resembled the community of the donor. FMT treatment was also associated with marked, yet temporary, alleviation of the recipient's abnormal bowel movements, suggesting a broader impact on gut health. Our results provide valuable preliminary evidence that FMT treatments can augment the recipient's gut microbiome, with potential implications for animal health and management.

Effect of partially hydrolyzed polyacrylamide (HPAM) on the bacterial communities of wetland rhizosphere soils and their efficiency in HPAM and alkane degradation

The effect of partially hydrolyzed polyacrylamide (HPAM) on structure and function of rhizosphere soil bacterial communities in constructed wetlands has been largely underinvestigated. In this study, we compare the effect of 250, 500, and 1000 mg/L of HPAM on bacterial community composition of Phragmites australis associated rhizosphere soils in an experimental wetland using MiSeq amplicon sequencing. Rhizosphere soils from the HPAM-free and the 500-mg/L-exposed treatments were used for laboratory experiments to further investigate the effect of HPAM on the soil's degradation and respiration activities. Soils treated with HPAM showed differences in bacterial communities with the dominance of Proteobacteria and the enrichment of potential hydrocarbon and HPAM-degrading bacteria. CO₂ generation was higher in the HPAM-free soils than in the HPAM pre-exposed soil, with a noticeable increase in both soils when oil was added. The addition of HPAM at different concentrations had a more pronounced effect on CO₂ evolution in the HPAM-pre-exposed soil. Soils were able to degrade between 37 ± 18.0 and 66 ± 6.7% of C₁₀ to C₃₀ alkanes after 28 days, except in the case of HPAM-pre-exposed soil treated with 500 mg/L where degradation reached 92 ± 4.3%. Both soils reduced HPAM concentration by 60 ± 15% of the initial amount in the 500 mg/L treatment, but by only ≤ 21 ± 7% in the 250-mg/L and 1000-mg/L treatments. In conclusion, the rhizosphere soils demonstrated the ability to adapt and retain their ability to degrade hydrocarbon in the presence of HPAM.

Transfer of Nitrogen and Phosphorus From Cattle Manure to Soil and Oats Under Simulative Cattle Manure Deposition

Simulated cattle manure deposition was used to estimate nutrient transfer to soil and oats and to investigate changes in microbial community composition and functional groups in oat rhizospheres. Nutrient absorption and return efficiency were calculated as a series of standard calculation formulas, and total nutrient transfer efficiency was nutrient absorption efficiency plus nutrient return efficiency. In total, 74.83% of nitrogen (N) and 59.30% of phosphorus (P) in cattle manure were transferred to soil and oats, with 11.79% of N and 7.89% of P in cattle manure absorbed by oats, and the remainder sequestered in the soil for 80 days after sowing. Cattle manure increased oat root length, surface, and volume under 0.2 mm diameter, and improved relative abundance of the microbiome known to be beneficial. In response to cattle manure, several bacteria known to be beneficial, such as Proteobacteria, Bacteroidota, and Firmicutes at phyla the level and Pseudoxanthomonas, Pseudomonas, and Sphingomonas at the genus level, were positively related to oat biomass and nutrient accumulation. For fungal communities, the relative abundance of Ascomycota is the predominant phylum, which varied in a larger range in the control treatment (81.0–63.3%) than the cattle manure deposition treatment (37.0–42.9%) as plant growing days extend. The relevant abundance of Basidiomycota known as decomposer was higher in cattle manure deposition treatment compared to that in control treatment at 15 days after sowing. More importantly, cattle manure deposition inhibited trophic mode within pathotroph like Alternaria and Fusarium fungal genus and promoted saprotroph and symbiotroph.

Nitrogen Addition Effects on Wetland Soils Depend on Environmental Factors and Nitrogen Addition Methods: A Meta-Analysis

Identifying the effects of nitrogen (N) addition under key environmental factors and N addition methods can aid in understanding the paradigm of N addition in wetland ecosystems. In this study, we conducted a meta-analysis of 30 field studies of wetland ecosystems and selected 14 indicators. We found that the changes in soil TN and SOC contributed significantly to the changes in microbial community structure under N additions. The environmental factors and N addition methods altered the direction or size of N addition effects on wetland soil properties, microbial diversity and key C and N cycling genes. N-limited conditions and climate conditions determined the N addition effect direction on SOC, and saline-alkali conditions determined the N addition effect direction on microbial diversity and AOB abundance. Environmental heterogeneity and N addition methods determine the response of wetland soil to nitrogen application. Therefore, it is crucial to study the effects of environmental factors and N addition methods on the N deposition of wetland soils.

Effects of Litter Decomposition on Soil N in Picea mongolica Forest at Different Forest Ages

In order to study the effects of litter decomposition on soil nitrogen of Piceamongolica in different forest ages, young forest (0–5a), middle-aged forest (5–30a), and near-mature forest (30–40a) stands were selected in the Baiyinaobao National Nature Reserve. Litter decomposition was assessed using the decomposition bag method. The seasonal and vertical spatial variation characteristics of total N, NH4+—N, and NO3−—N caused by litter decomposition in P. mongolica forest soil were studied for different stand ages. Results showed that: (1) There was a positive correlation between litter N content and soil organic matter, total N content, and NO3−—N content across different forest ages (p < 0.05). There was a negative correlation between litter N and NH4+—N contents. A negative correlation between litter C content and soil organic matter, total N, and NO3−—N contents was also observed. (2) In this study, the total N and NO3−—N increased with the increase in N content during litter decomposition.NH4+—N in the soil was positively correlated with sample date, soil NO3−—N, and forest age (p < 0.05), and negatively correlated with soil depth (p < 0.01). NO3−—N in the soil was negatively correlated with sample date and forest age (p < 0.05), and significantly negatively correlated with soil depth (p < 0.01). (3) the NH4+—N content is greater than that of NO3−—N in each soil layer for the three forest ages. The correlation analysis indicated which factors influenced NH4+—N and NO3−—N in the soil. The content decreased during February and November and increased in May and August. (4) The total N, NH4+—N, and NO3−—N in the forest soils across the three forest ages increased with the depth of the soil layer (0–50 cm) and showed an overall downward trend. The contents of NH4+—N in the soil layer from the young forest (0–10 cm, 10–20 cm and 20–30 cm, 30–40 cm, and 40–50 cm) differed significantly (p < 0.05), as did the NO3−—N results (p < 0.05), while results from the middle-aged forest and near-mature forest increased with soil layer depth. There was no significant difference in the NH4+—N soil content. (5) The NH4+—N in the forest soils showed a trend from mature forest > middle-aged forest > young forest. This trend for soil NO3−—N content is consistent with that of the NH4+—N content in the Picea mongolica forest soil.

The combined effect of short-term hydrological and N-fertilization manipulation of wetlands on CO2, CH4, and N2O emissions

Freshwater wetlands are natural sinks of carbon; yet, wetland conversion for agricultural uses can shift these carbon sinks into large sources of greenhouse gases. We know that the anthropogenic alteration of wetland hydrology and the broad use of N-fertilizers can modify biogeochemical cycling, however, the extent of their combined effect on greenhouse gases exchange still needs further research. Moreover, there has been recent interest in wetlands rehabilitation and preservation by improving natural water flow and by seeking alternative solutions to nutrient inputs. In a microcosm setting, we experimentally exposed soils to three inundation treatments (Inundated, Moist, Drained) and a nutrient treatment by adding high nitrogen load (300 kg ha^-1) to simulate physical and chemical disturbances. After, we measured the depth microprofiles of N₂O and O₂ concentration and CO₂ and CH₄ emission rates to determine how hydrological alteration and nitrogen input affect carbon and nitrogen cycling processes in inland wetland soils. Compared to the Control soils, N-fertilizer increased CO₂ emissions by 40% in Drained conditions and increased CH₄ emissions in Inundated soils over 90%. N₂O emissions from Moist and Inundated soils enriched with nitrogen increased by 17.4 and 18-fold, respectively. Overall, the combination of physical and chemical disturbances increased the Global Warming Potential (GWP) by 7.5-fold. The first response of hydrological rehabilitation, while typically valuable for CO₂ emission reduction, amplified CH₄ and N₂O emissions when combined with high nitrogen inputs. Therefore, this research highlights the importance of evaluating the potential interactive effects of various disturbances on biogeochemical processes when devising rehabilitation plans to rehabilitate degraded wetlands.

Uptake and Accumulation of Nano/Microplastics in Plants: A Critical Review

The ubiquitous presence of microplastics (MPs) and nanoplastics (NPs) in the environment is an undeniable and serious concern due to their higher persistence and extensive use in agricultural production. This review highlights the sources and fate of MPs and NPs in soil and their uptake, translocation, and physiological effects in the plant system. We provide the current snapshot of the latest reported studies with the majority of literature spanning the last five years. We draw attention to the potential risk of MPs and NPs in modern agriculture and their effects on plant growth and development. We also highlight their uptake and transport pathways in roots and leaves via different exposure methods in plants. Conclusively, agricultural practices, climate changes (wet weather and heavy rainfall), and soil organisms play a major role in transporting MPs and NPs in soil. NPs are more prone to enter plant cell walls as compared to MPs. Furthermore, transpiration pull is the dominant factor in the plant uptake and translocation of plastic particles. MPs have negligible negative effects on plant physiological and biochemical indicators. Overall, there is a dire need to establish long-term studies for a better understanding of their fate and associated risks mechanisms in realistic environment scenarios for safe agricultural functions.

Spatially resolved correlative microscopy and microbial identification reveal dynamic depth- and mineral-dependent anabolic activity in salt marsh sediment

Coastal salt marshes are key sites of biogeochemical cycling and ideal systems in which to investigate the community structure of complex microbial communities. Here, we clarify structural-functional relationships among microorganisms and their mineralogical environment, revealing previously undescribed metabolic activity patterns and precise spatial arrangements within salt marsh sediment. Following 3.7-day in situ incubations with a non-canonical amino acid that was incorporated into new biomass, samples were resin-embedded and analysed by correlative fluorescence and electron microscopy to map the microscale arrangements of anabolically active and inactive organisms alongside mineral grains. Parallel sediment samples were examined by fluorescence-activated cell sorting and 16S rRNA gene sequencing to link anabolic activity to taxonomic identity. Both approaches demonstrated a rapid decline in the proportion of anabolically active cells with depth into salt marsh sediment, from ~60% in the top centimetre to 9.4%-22.4% between 2 and 10 cm. From the top to the bottom, the most prominent active community members shifted from sulfur cycling phototrophic consortia, to putative sulfate-reducing bacteria likely oxidizing organic compounds, to fermentative lineages. Correlative microscopy revealed more abundant (and more anabolically active) organisms around non-quartz minerals including rutile, orthoclase and plagioclase. Microbe-mineral relationships appear to be dynamic and context-dependent arbiters of biogeochemical cycling.

Organic Amendments Alter Soil Hydrology and Belowground Microbiome of Tomato (Solanum lycopersicum)

Manure-derived organic amendments are a cost-effective tool that provide many potential benefits to plant and soil health including fertility, water retention, and disease suppression. A greenhouse experiment was conducted to evaluate how dairy manure compost (DMC), dairy manure compost-derived vermicompost (VC), and dehydrated poultry manure pellets (PP) impact the tripartite relationship among plant growth, soil physiochemical properties, and microbial community composition. Of tomato plants with manure-derived fertilizers amendments, only VC led to vigorous growth through the duration of the experiment, whereas DMC had mixed impacts on plant growth and PP was detrimental. Organic amendments increased soil porosity and soil water holding capacity, but delayed plant maturation and decreased plant biomass. Composition of bacterial communities were affected more by organic amendment than fungal communities in all microhabitats. Composition of communities outside roots (bulk soil, rhizosphere, rhizoplane) contrasted those within roots (endosphere). Distinct microbial communities were detected for each treatment, with an abundance of Massilia, Chryseolinea, Scedosporium, and Acinetobacter distinguishing the control, vermicompost, dairy manure compost, and dehydrated poultry manure pellet treatments, respectively. This study suggests that plant growth is affected by the application of organic amendments not only because of the soil microbial communities introduced, but also due to a synergistic effect on the physical soil environment. Furthermore, there is a strong interaction between root growth and the spatial heterogeneity of soil and root-associated microbial communities.

Effect of microplastics and arsenic on nutrients and microorganisms in rice rhizosphere soil

The presence of microplastics and arsenic in soil can endanger crop growth; therefore, their effects on the properties of rhizosphere soil should be evaluated. Large (10-100 µm) and small (0.1-1 µm) polystyrene (PSMP) and polytetrafluorethylene (PTFE) particles were added to soil with different arsenic concentrations (1.4, 24.7, and 86.3 mg kg^-1) to investigate the combined effect of microplastics and arsenic pollution on rice rhizosphere soil. After the addition of PSMP and PTFE, pH, arsenic (V) and arsenic (III) in the soil were observed to decrease. The interaction of arsenic with PSMP and PTFE resulted in this phenomenon, leading to a decrease of arsenic bioavailability in the soil. PSMP, PTFE, and arsenic reduced the abundance of Proteobacteria, increased the abundance of Chloroflexi and Acidobacteria, and inhibited soil urease, acid phosphatase, protease, dehydrogenase, and peroxidase activity via affecting the tertiary structure of the enzyme. PSMP, PTFE, and arsenic also reduced the available nitrogen and phosphorus content in the soil. Arsenic increased the soil organic matter content, whereas PSMP and PTFE reduced the organic matter content. Furthermore, microplastics inhibited the effects of arsenic on the microbial and chemical properties of the rhizosphere soil. This study revealed the effects of microplastic and arsenic pollution on rice rhizosphere microorganisms and nutrients, and elucidated the mechanism by which these pollutants retard crop growth in the designed growth medium.

Effects of organic matter addition on chronically hydrocarbon-contaminated soil

Soil is the recipient of organic pollutants as a consequence of anthropogenic activities. Hydrocarbons are contaminants that pose a risk to human and environmental health. Bioremediation of aging contaminated soils is a challenge due to the low biodegradability of contaminants as a result of their interaction with the soil matrix. The aim of this work was to evaluate the effect of both composting and the addition of mature compost on a soil chronically contaminated with hydrocarbons, focusing mainly on the recovery of soil functions and transformations of the soil matrix as well as microbial community shifts. The initial pollution level was 214 ppm of polycyclic aromatic hydrocarbons (PAHs) and 2500 ppm of aliphatic hydrocarbons (AHs). Composting and compost addition produced changes on soil matrix that promoted the release of PAHs (5.7 and 15 % respectively) but not the net PAH elimination. Interestingly, composting stimulated AHs elimination (about 24 %). The lack of PAHs elimination could be attributed to the insufficient PAHs content to stimulate the microbial degrading capacity, and the preferential consumption of easily absorbed C sources by the bacterial community. Despite the low PAH catabolic potential of the aging soil, metabolic shift was driven by the addition of organic matter, which could be monitored by the ratio of Proteobacteria to Actinobacteria combined with E₄/E₆ ratio. Regarding the quality of the soil, the nutrients provided by the exogenous organic matter contributed to the recovery of the global functions and species diversity of the soil along with the reduction of phytotoxicity.

Potentilla anserina L. developmental changes affect the rhizosphere prokaryotic community

Plant roots and soil prokaryotes primarily interact with each other in the rhizosphere. Changes in the rhizosphere prokaryotic structure are influenced by several factors. In this study, the community structure of the Potentilla anserina L. rhizosphere prokaryotes was identified and evaluated by high-throughput sequencing technology in different continuous cropping fields and developmental stages of the plant. In total, 2 archaeal (Euryarchaeota and Thaumarchaeota) and 26 bacterial phyla were identified in the P. anserina rhizosphere. The bacterial community was mainly composed of Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Planctomycetes, Proteobacteria, and Verrucomicrobia. Moreover, the prokaryotic community structure of the rhizosphere varied significantly during plant development. Our results provide new insights into the dynamics of the P. anserina rhizosphere prokaryotic community and may provide useful information for enhancing the growth and development of P. anserina through artificial control of the soil prokaryotes.

Hidden heterogeneity and co-occurrence networks of soil prokaryotic communities revealed at the scale of individual soil aggregates

Sequencing PCR‐amplified gene fragments from metagenomic DNA is a widely applied method for studying the diversity and dynamics of soil microbial communities. Typically, DNA is extracted from 0.25 to 1 g of soil. These amounts, however, neglect the heterogeneity of soil present at the scale of soil aggregates and thus ignore a crucial scale for understanding the structure and functionality of soil microbial communities. Here, we show with a nitrogen‐depleted agricultural soil the impact of reducing the amount of soil used for DNA extraction from 250 mg to approx. 1 mg to access spatial information on the prokaryotic community structure, as indicated by 16S rRNA gene amplicon analyses. Furthermore, we demonstrate that individual aggregates from the same soil differ in their prokaryotic community compositions. The analysis of 16S rRNA gene amplicon sequences from individual soil aggregates allowed us, in contrast to 250 mg soil samples, to construct a co‐occurrence network that provides insight into the structure of microbial associations in the studied soil. Two dense clusters were apparent in the network, one dominated by Thaumarchaeota, known to be capable of ammonium oxidation at low N concentrations, and the other by Acidobacteria subgroup 6, representing an oligotrophic lifestyle to obtain energy from SOC. Overall this study demonstrates that DNA obtained from individual soil aggregates provides new insights into how microbial communities are assembled.

Deciphering the rhizosphere microbiome of a bamboo plant in response to different chromium contamination levels

Bamboo has been considered a potential plant species for phytoremediation due to its high biomass and heavy metal (HM) resistance. However, little is known about the interactions between bamboo and soil microbial activities in HM-contaminated soils. Here, we investigated the characteristics of microbial communities in the rhizosphere soil of Lei bamboo (Phyllostachys praecox) along a chromium (Cr) gradient. We found that the soil Cr content was positively correlated with the total organic carbon (TOC) and HCl-extractable Cr but negatively correlated with the pH and bacterial and fungal Shannon indices. Proteobacteria and Ascomycota predominated in the bamboo rhizosphere under Cr pollution. A co-occurrence network showed that two of the most Cr-sensitive bacterial genera and keystone taxa were from the Acidobacteria, indicating that this phylum can be as an indicator for the studied Cr-polluted soils. Redundancy analysis revealed that both the soil bacterial and fungal community compositions were significantly correlated (p < 0.05) with Cr, pH, TOC, alkali-hydrolysable N (AN), and available phosphorus (AP). The increase in TOC as the Cr content increased can be ascribed to an adverse Cr effect on the soil microflora, probably because the microbial biomass was less effective in mineralizing soil C under Cr-polluted conditions.

Identification of nitrogen-incorporating bacteria in a sequencing batch reactor: A combining cultivation-dependent and cultivation-independent method

Nitrogen-incorporating bacteria in activated sludge play important roles in nitrogen removal in sequencing bactch reactor (SBR), but the active microorganisms and their interactions in the complex community are rarely revealed. Herein, a combining cultivation-dependent and cultivation-independent methods associated with DNA-stable-isotope probing (SIP) was applied to determine the microbes responsible for nitrogen-incorporating in SBR. Results revealed that Cytophagaceae and Sphingobacteriales were identified to be involved in nitrification, and Anaerolineae, Plasticicumulans and Elusimicrobia were responsible for denitrification. Cultivable nitrobacter and denitrifiers were isolated from the activated sludge, but they did not participate in the nitrogen-incorporating based on the SIP results. Additionally, the molecular ecological network analysis indicated that the SIP-identified nitrogen-incorporating bacteria exhibited more links with the intra-community, which might explain the failure of isolating these active bacteria. These findings add understanding of the removal of nitrogenous compounds drived by nitrogen-incorporating bacteria in actual wastewater treatment process.

Bacterial Community Dynamics Distinguish Poultry Compost from Dairy Compost and Non-Amended Soils Planted with Spinach

The aim of this study was to determine whether and how poultry litter compost and dairy manure compost alter the microbial communities within field soils planted with spinach. In three successive years, separate experimental plots on two fields received randomly assigned compost treatments varying in animal origin: dairy manure (DMC), poultry litter (PLC), or neither (NoC). The composition and function of bacterial and fungal communities were characterized by the amplicon sequencing of marker genes and by the ecoenzyme activity, respectively. The temporal autocorrelation within and among years was adjusted by principal response curves (PRC) to analyze the effect of compost on community composition among treatments. Bacteria in the phylum Bacteriodetes, classes Flavobacteriia and Spingobacteriales (Fluviicola, Flavobacteriia, and Pedobacter), were two to four times more abundant in soils amended with PLC than DMC or NoC consistently among fields and years. Fungi in the phylum Ascomycota were relatively abundant, but their composition was field-specific and without treatment differences. The ecoenzyme data verify that the effects of PLC and DMC on soil communities are based on their microbial composition and not a response to the C source or nutrient content of the compost.

Effects of Different Fertilizer Treatments on Rhizosphere Soil Microbiome Composition and Functions

Fertilization influences the soil microbiome. However, little is known about the effects of long-term fertilization on soil microbial metabolic pathways. In this study, we investigated the soil microbiome composition and function and microbial participation in the N cycle according to the Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) functional annotation of different genes in a metagenomic analysis after long-term fertilization. Fertilizer application significantly changed the soil C/N ratio. Chemical fertilizer (NPK) treatment decreased soil pH, and chemical fertilizer combined with straw (NPK+S0.5) treatment increased ammonium nitrogen (NH4+-N) but decreased nitrate nitrogen (NO3−-N). NPK, NPK+S0.5 and S0.5 applications did not change the soil microbiome composition or dominant phylum but changed the relative abundances of microbiome components. Moreover, fertilizer significantly influenced metabolic processes, cellular processes and single-organism processes. Compared with a no-fertilizer treatment (CK), the NPK treatment resulted in more differentially expressed gene (DEG) pathways than the NPK+S0.5 and S0.5 treatments, and these pathways significantly correlated with soil nitrate nitrogen (NO3−-N), available phosphorus (AP) and the moisture content of soil (MC). KEGG analysis found that fertilizer application mainly affected the ribosome, photosynthesis and oxidative phosphorylation pathways. S0.5 and NPK+S0.5 increased microbial nitrogen fixation, and NPK and NPK+S0.5 decreased amoA and amoB and accelerated denitrification. Thus, organic fertilizer increased N fixation and nitrification, and inorganic N fertilizer accelerated denitrification. We found that the function of the soil microbiome under different fertilizer applications could be important for the rational application of fertilizer and for environmental and sustainable development.

The importance of edaphic niches functionality for the sustainability of phytomanagement in semiarid mining impacted ecosystems

Mining activities on metal sulphide ores are considered one of the most environmentally damaging anthropogenic activities worldwide, mainly due to the production of metal(loid)- enriched tailings. The objective of the work was to elucidate which factors, including edaphic, vegetation and microbiological aspects, determine soil functionality in the phytomagement of mine tailings piles in semiarid areas. For this purpose, a field study was conducted using a transect experimental design in a former mining area located in southern Spain. Soil characteristics, including edaphic parameters, bacterial and fungal compositions, were determined. The variation in edaphic parameters (pH, electrical conductivity, organic carbon, particle size distribution, etc) through the deterioration transect caused a decrease in plant and microbial diversities, as well as in microbial productivity measured by enzymatic activities. Variation in bacterial relative abundances through the transect was better explained by soil fertility related factors, such as organic matter, pH, salinity, enzymatic activities or microbial biomass (which in turn were related to the presence of plants), than by metals concentrations. The presence of vegetation at the tailings allowed the transition from lithotrophic bacterial orders which dominated in bare tailings areas (e.g. Acidimicrobiales, Chromatiales) to organotrophic oriented orders (e.g. Cytophagales, Actinomycetales). Vegetated patches at the tailings pile and its borders shared some organotrophic bacteria with control forest samples (e.g. Rhizobiales), indicating that natural plant mediated successional processes might stimulate biogeochemical cycles similar to those occurring at non-polluted systems. This functionality of the impacted sites, which include unfavourable edaphic conditions, should be taken into account in the phytomanagement of mine tailings, since it may support its long-term sustainability. Unlike bacteria, variations in fungal relative abundances through the transect were not clearly explained by soil parameters or the presence of plants. Other factors related to spatial distribution or the type of organic substrates may be more determinant in the case of fungi.

Under the Christmas Tree: Belowground Bacterial Associations With Abies nordmanniana Across Production Systems and Plant Development

Abies nordmanniana is an economically important tree crop widely used for Christmas tree production. After initial growth in nurseries, seedlings are transplanted to the field. Rhizosphere bacterial communities generally impact the growth and health of the host plant. However, the dynamics of these communities during A. nordmanniana growth in nurseries, and during transplanting, has not previously been addressed. By a 16S rRNA gene amplicon sequencing approach, we characterized the composition and dynamics of bacterial communities in the rhizosphere during early plant growth in field and greenhouse nurseries and for plants transplanted from the greenhouse to the field. Moreover, the N-cycling potential of rhizosphere bacteria across plant age was addressed in both nurseries. Overall, a rhizosphere core microbiome of A. nordmanniana, comprising 19.9% of the taxa at genus level, was maintained across plant age, nursery production systems, and even during the transplantation of plants from the greenhouse to the field. The core microbiome included the bacterial genera Bradyrhizobium, Burkholderia, Flavobacterium, Pseudomonas, Rhizobium, Rhodanobacter, and Sphingomonas, which harbor several N-fixing and plant growth–promoting taxa. Nevertheless, both plant age and production system caused significant changes in the rhizosphere bacterial communities. Concerning community composition, the relative abundance of Rhizobiales (genera Rhizobium, Bradyrhizobium, and Devosia) was higher in the rhizosphere of field-grown A. nordmanniana, whereas the relative abundance of Enterobacteriales and Pseudomonadales (genus Pseudomonas) was higher in the greenhouse. Analysis of community dynamics across plant age showed that in the field nursery, the most abundant bacterial orders showed more dynamic changes in their relative abundance in the rhizosphere than in the bulk soil. In the greenhouse, age-dependent dynamics even occurred but affected different taxa than for the field-grown plants. The N-cycling potential of rhizosphere bacterial communities showed an increase of the relative abundance of genes involved in nitrogen fixation and denitrification by plant age. Similarly, the relative abundance of reported nitrogen-fixing or denitrifying bacteria increased by plant age. However, different community structures seemed to lead to an increased potential for nitrogen fixation and denitrification in the field versus greenhouse nurseries.

Genome sequencing as a new window into the microbial community of membrane bioreactors - A critical review

Recent developed sequencing techniques have resulted in a new and unprecedented way to study biological wastewater treatment, in which most organisms are uncultivable. This review provides (i) an insight on state-of-the-art sequencing techniques and their limitations; (ii) a critical assessment of the microbial community in biological reactor and biofouling layer in a membrane bioreactor (MBR). The data from high-throughput sequencing has been used to infer microbial growth conditions and metabolisms of microorganisms present in MBRs at the time of sampling. These data shed new insight to two fundamental questions about a microbial community in the MBR process namely the microbial composition (who are they?) and the functions of each specific microbial assemblage (what are their function?). The results to date also highlight the complexity of the microbial community growing on MBRs. Environmental conditions are dynamic and diverse, and can influence the diversity and structural dynamics of any given microbial community for wastewater treatment. The benefits of understanding the structure of microbial communities on three major aspects of the MBR process (i.e. nutrient removal, biofouling control, and micropollutant removal) were symmetrically delineated. This review also indicates that the deployment of microbial community analysis for a practical engineering context, in terms of process design and system optimization, can be further realized.

Quantification of denitrifier genes population size and its relationship with environmental factors

The objectives of this study were to use real-time PCR for culture-independent quantification of the copy numbers of 16S rRNA and denitrification functional genes, and also the relationships between gene copy numbers and soil physicochemical properties. In this study, qPCR analysis of the soil samples showed 16S rRNA, nirS, nirK, nosZI and nosZII average densities of 3.0 × 10⁸, 2.25 × 10⁷, 2.9 × 10⁵, 4.0 × 10⁶ and 1.75 × 10⁷ copies per gram of dry soil, respectively. In addition, the abundances of (nirS + nirK), nosZI and nosZII relative to 16S rRNA genes were 1.4-34.1%, 0.06-3.95% and 1.3-39%, respectively, confirming the low proportion of denitrifiers to total bacteria in soil. This showed that the non-denitrifying nosZII-type bacteria may contribute significantly to N₂O consumption in the soil. Furthermore, the shifts in abundance and diversity of the total bacteria and denitrification functional gene copy numbers correlated significantly with the various soil factors. It is the first study in Turkey about the population size of denitrification functional genes in different soil samples. It also aims to draw attention to nitrous oxide-associated global warming.

Anaerobically digested blackwater treatment by simultaneous denitrification and anammox processes: Feeding loading affects reactor performance and microbial community succession

Source diverted blackwater collected from toilets can be anaerobically digested to recover energy. The anaerobically digested blackwater (ADB) contains high levels of ammonium and low carbon to nitrogen (C/N) ratio. In the present study, ADB was treated by a two-stage nitritation-denitrification/anammox process in an integrated fixed film activated sludge-continuous flow reactor (IFAS-CFR). NH₄⁺-N, NO₂^--N, total nitrogen (TN), and chemical oxygen demand (COD) removal efficiencies were 80%, 82%, 76%, and 78%, respectively. Anaerobic ammonium oxidation (anammox) and denitrification contributed to 44-48%, and 52-56% of total nitrogen removal, respectively. Both of the protein- and humic acid-like matters were removed during the process. An increase in feed load promoted the sustained growth of anammox bacteria-Candidatus Brocadia in the biofilm, as well as an increase of denitrifiers (Pseudomonas, Thermotonus, Phodanobacter, Caulobacter) in both biofilm and suspended biomass, which remained higher in the suspended biomass than in biofilm. Overall, biofilm had higher nitrogen removal efficiency than suspended biomass, while suspended biomass had a higher COD removal efficiency than biofilm.

Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades

BACKGROUND

Currently, much is unknown about the taxonomic diversity and the mechanisms of methane metabolism in the Florida Everglades ecosystem. The Loxahatchee National Wildlife Refuge is a section of the Florida Everglades that is almost entirely unstudied in regard to taxonomic profiling. This short report analyzes the metagenome of soil samples from this Refuge to investigate the predominant taxa, as well as the abundance of genes involved in environmentally significant metabolic pathways related to methane production (nitrogen fixation and dissimilatory sulfite reduction).

METHODS

Shotgun metagenomic sequencing using the Illumina platform was performed on 17 soil samples from four different sites within the Loxahatchee National Wildlife Refuge, and underwent quality control, assembly, and annotation. The soil from each sample was tested for water content and concentrations of organic carbon and nitrogen.

RESULTS

The three most common phyla of bacteria for every site were Actinobacteria, Acidobacteria, and Proteobacteria; however, there was variation in relative phylum composition. The most common phylum of Archaea was Euryarchaeota for all sites. Alpha and beta diversity analyses indicated significant congruity in taxonomic diversity in most samples from Sites 1, 3, and 4 and negligible congruity between Site 2 and the other sites. Shotgun metagenomic sequencing revealed the presence of biogeochemical biomarkers of particular interest (e.g., mrcA, nifH, and dsrB) within the samples. The normalized abundances of mcrA, nifH, and dsrB exhibited a positive correlation with nitrogen concentration and water content, and a negative correlation with organic carbon concentration.

CONCLUSION

This Everglades soil metagenomic study allowed examination of wetlands biological processes and showed expected correlations between measured organic constituents and prokaryotic gene frequency. Additionally, the taxonomic profile generated gives a basis for the diversity of prokaryotic microbial life throughout the Everglades.

Organic amendment strengthens interkingdom associations in the soil and rhizosphere of barley (Hordeum vulgare)

Anthropogenic modification of soil systems has diverse impacts on food web interactions and ecosystem functioning. To understand the positive, neutral or adverse effects of agricultural practices on the associations of community members of soil microbes and microfaunal biomes, we characterized the effects of different fertilization types (organic, inorganic and a combination of organic and inorganic) on the food web active communities in the bulk soil and rhizosphere compartments in field conditions. We examined the influence of fertilization on (i) individual groups (bacteria, protozoa and fungi as microbe representatives and metazoans as microfauna representatives) and (ii) inter-kingdom interactions (focusing on the interactions between bacteria and eukaryotic groups) both neglecting and considering environmental factors in our analysis in combination with the microbial compositional data. Our results revealed different patterns of biota communities under organic versus inorganic fertilization, which shaped food web associations in both the bulk and rhizosphere compartments. Overall, organic fertilization increased the complexity of microbial-microfaunal ecological associations with inter- and intra- connections among categories of primary decomposers (bacteria and fungi) and predators (protozoa and microfauna) and differences in potential function in the soil food web in both the bulk and rhizosphere compartments. Furthermore, the inter-connections between primary decomposers and predators in bulk soil were more pronounced when environmental factors were considered. We suggest that organic fertilization selects bacterial orders with different potential ecological functions and interactions as survival, predation and cooperation due to more complex environment than those of inorganic or combined fertilization. Our findings support the importance of a comprehensive understanding of trophic food web patterns for soil management systems.

Metabolic Overlap in Environmentally Diverse Microbial Communities

The majority of microbial communities consist of hundreds to thousands of species, creating a massive network of organisms competing for available resources within an ecosystem. In natural microbial communities, it appears that many microbial species have highly redundant metabolisms and seemingly are capable of utilizing the same substrates. This is paradoxical, as theory indicates that species requiring a common resource should outcompete one another. To better understand why microbial species can coexist, we developed metabolic overlap (MO) as a new metric to survey the functional redundancy of microbial communities at the genome scale across a wide variety of ecosystems. Using metagenome-assembled genomes, we surveyed nearly 1,000 studies across nine ecosystem types. We found the highest MO in extreme (i.e., low pH/high temperature) and aquatic environments, while the lowest MO was observed in communities associated with animal hosts, the built/engineered environment, and soil. In addition, different metabolism subcategories were explored for their degree of MO. For instance, overlap in nitrogen metabolism was among the lowest in animal and engineered ecosystems, while species from the built environment had the highest overlap. Together, we present a metric that utilizes whole genome information to explore overlapping niches of microbes. This provides a detailed picture of potential metabolic competition and cooperation between species present in an ecosystem, indicates the main substrate types sustaining the community, and serves as a valuable tool to generate hypotheses for future research.

The Water Hyacinth Microbiome: Link Between Carbon Turnover and Nutrient Cycling

Water hyacinth (WH), a large floating plant, plays an important role in the biogeochemistry and ecology of many freshwaters globally. Its biogeochemical impact on wetland functioning is strongly mediated by the microbiome associated with its roots. However, little is known about the structure and function of this WH rhizobiome and its relation to wetland ecosystem functioning. Here, we unveil the core and transient rhizobiomes of WH and their key biogeochemical functions in two of the world's largest wetlands: the Amazon and the Pantanal. WH hosts a highly diverse microbial community shaped by spatiotemporal changes. Proteobacteria lineages were most common, followed by Actinobacteria and Planctomycetes. Deltaproteobacteria and Sphingobacteriia predominated in the core microbiome, potentially associated with polysaccharide degradation and fermentation of plant-derived carbon. Conversely, a plethora of lineages were transient, including highly abundant Acinetobacter, Acidobacteria subgroup 6, and methanotrophs, thus assuring diverse taxonomic signatures in the two different wetlands. Our findings point out that methanogenesis is a key driver of, and proxy for, community structure, especially during seasonal plant decline. We provide ecologically relevant insights into the WH microbiome, which is a key element linking plant-associated carbon turnover with other biogeochemical fluxes in tropical wetlands.

Geomicrobiology of a seawater-influenced active sulfuric acid cave

Fetida Cave is an active sulfuric acid cave influenced by seawater, showing abundant microbial communities that organize themselves under three main different morphologies: water filaments, vermiculations and moonmilk deposits. These biofilms/deposits have different cave distribution, pH, macro- and microelement and mineralogical composition, carbon and nitrogen content. In particular, water filaments and vermiculations had circumneutral and slightly acidic pH, respectively, both had abundant organic carbon and high microbial diversity. They were rich in macro- and microelements, deriving from mineral dissolution, and, in the case of water filaments, from seawater composition. Vermiculations had different color, partly associated with their mineralogy, and unusual minerals probably due to trapping capacities. Moonmilk was composed of gypsum, poor in organic matter, had an extremely low pH (0-1) and low microbial diversity. Based on 16S rRNA gene analysis, the microbial composition of the biofilms/deposits included autotrophic taxa associated with sulfur and nitrogen cycles and biomineralization processes. In particular, water filaments communities were characterized by bacterial taxa involved in sulfur oxidation and reduction in aquatic, aphotic, microaerophilic/anoxic environments (Campylobacterales, Thiotrichales, Arenicellales, Desulfobacterales, Desulforomonadales) and in chemolithotrophy in marine habitats (Oceanospirillales, Chromatiales). Their biodiversity was linked to the morphology of the water filaments and their collection site. Microbial communities within vermiculations were partly related to their color and showed high abundance of unclassified Betaproteobacteria and sulfur-oxidizing Hydrogenophilales (including Sulfuriferula), and Acidiferrobacterales (including Sulfurifustis), sulfur-reducing Desulfurellales, and ammonia-oxidizing Planctomycetes and Nitrospirae. The microbial community associated with gypsum moonmilk showed the strong dominance (>60%) of the archaeal genus Thermoplasma and lower abundance of chemolithotrophic Acidithiobacillus, metal-oxidizing Metallibacterium, Sulfobacillus, and Acidibacillus. This study describes the geomicrobiology of water filaments, vermiculations and gypsum moonmilk from Fetida Cave, providing insights into the microbial taxa that characterize each morphology and contribute to biogeochemical cycles and speleogenesis of this peculiar seawater-influenced sulfuric acid cave.

Tomato plants rather than fertilizers drive microbial community structure in horticultural growing media

Synthetic fertilizer production is associated with a high environmental footprint, as compounds typically dissolve rapidly leaching emissions to the atmosphere or surface waters. We tested two recovered nutrients with slower release patterns, as promising alternatives for synthetic fertilizers: struvite and a commercially available organic fertilizer. Using these fertilizers as nitrogen source, we conducted a rhizotron experiment to test their effect on plant performance and nutrient recovery in juvenile tomato plants. Plant performance was significantly improved when organic fertilizer was provided, promoting higher shoot biomass. Since the microbial community influences plant nitrogen availability, we characterized the root-associated microbial community structure and functionality. Analyses revealed distinct root microbial community structure when different fertilizers were supplied. However, plant presence significantly increased the similarity of the microbial community over time, regardless of fertilization. Additionally, the presence of the plant significantly reduced the potential ammonia oxidation rates, implying a possible role of the rhizosheath microbiome or nitrification inhibition by the plant. Our results indicate that nitrifying community members are impacted by the type of fertilizer used, while tomato plants influenced the potential ammonia-oxidizing activity of nitrogen-related rhizospheric microbial communities. These novel insights on interactions between recovered fertilizers, plant and associated microbes can contribute to develop sustainable crop production systems.

Composts of poultry litter or dairy manure differentially affect survival of enteric bacteria in fields with spinach

AIMS

The aim was to determine the survival and persistence of Escherichia coli in soil amended with compost from different manure sources.

METHOD AND RESULTS

Complex interactions of abiotic and biotic factors on E. coli survival were characterized in field experiment plots receiving randomly assigned compost treatments: dairy windrow, dairy vermicompost, poultry windrow or no compost. Biomass, activity and function of indigenous microbial communities in the composts and soils were measured concurrently to determine whether mechanisms of compost were driven by biotic or abiotic properties. E. coli persisted in compost containing poultry amendments but not in composts containing dairy or no amendments. Poultry compost contained more NH₄ -N and a distinct microbial community compared to dairy and no compost treatments. A laboratory experiment performed on compost extracts suggested that E. coli survived better in extracts devoid of indigenous microbes as long as bioavailable nutrients were plentiful.

CONCLUSIONS

Dairy-based composts are less likely to support E. coli survival than poultry-based composts.

SIGNIFICANCE AND IMPACT OF THE STUDY

Results aid in risk assessment of the use of different types of manure-based compost and soil amendments in fruit and vegetable production by elucidating the roles of nutrient and microbial community composition on survival of E. coli in amended field soils.

'Concord' grapevine nutritional status and chlorosis rank associated with fungal and bacterial root zone microbiomes

Leaf chlorosis in vineyards is associated with reduced crop yields and quality. While iron (Fe) is understood to play a crucial role in chlorosis, total plant and soil Fe are not always indicative of chlorosis in grapevines. Physiology of chlorosis in vineyards has been well-studied, but the soil microbial consequences of and contributions to chlorosis have received little attention. We used next-generation sequencing (NGS) to examine the bacterial and fungal communities associated with grapevines demonstrating varying degrees of visual chlorosis symptoms. Additionally, chemical analyses of soils and grape leaves were used to explore the influence of plant nutritional status and soil chemistry on microbial community composition. Finally, factors influencing bacterial community composition were correlated with predicted bacterial community function. Leaf tissue magnesium (leaf Mg) concentrations and chlorosis rank were correlated with bacterial community composition as determined via dbRDA (distance-based Redundancy Analysis) using Bray-Curtis dissimilarities. Non-metric multidimensional scaling (NMDS) revealed a significant correlation between fungal community composition and soil Fe and pH, along with leaf N, Mg, and Ca (mg.kg^-1). Chlorosis rank was moderately correlated with KEGG Orthology (KO) terms associated with nitrogen (N) and carbon (C) metabolism in soils, while leaf Mg was associated with a spectrum of KO terms including glycosphingolipid biosynthesis, glycan degradation, transporters, and porphyrin and chlorophyll metabolism. Additionally, abundance of many bacterial operational taxonomic units was significantly correlated with leaf Mg, including those from the following orders: Rhodobacterales, Acidobacteriales, Opitutales, Sphingomonadales, Burkholderiales, Saprospirales, and Flavobacteriales. Our findings suggest grapevine chlorosis is interrelated with soil microbial community structure and function, plant nutrition, and soil chemistry.